/// <summary>
/// This parses a single row of data and adds it to a sequence.
/// </summary>
/// <param name="bioValidator"></param>
/// <param name="seqdataline"></param>
private void LoadSequenceData(IBioValidator bioValidator, Match seqdataline)
{
string rowName = seqdataline.Groups["Rowname"].Value;
Debug.Assert(!string.IsNullOrEmpty(rowName));
AE2Sequence sequence = (AE2Sequence)_sequences.FirstOrDefault(seq => string.Compare(seq.CommonName, rowName) == 0);
if (sequence == null)
{
sequence = new AE2Sequence(bioValidator)
{
CommonName = rowName, ScientificName = rowName
};
_sequences.Add(sequence);
}
// Get the data this represents.
int startIndex = Int32.Parse(seqdataline.Groups["Startindex"].Value);
// AE2 omits the blanks so skip anything we haven't seen with a gap.
if (sequence.AlignedData.Count < startIndex)
{
for (int i = 0; i < (startIndex - sequence.AlignedData.Count); i++)
{
sequence.AlignedData.Add(BioSymbol.Gap);
}
}
string seqdata = seqdataline.Groups["Seqdata"].Value;
for (int index = 0; index < seqdata.Length;)
{
IBioSymbol symbol;
if (seqdata[index] == '\\')
{
symbol = CharacterToBioSymbol(bioValidator, ConvertOctal(new[] { seqdata[index + 1], seqdata[index + 2], seqdata[index + 3] }));
index += 4;
}
else
{
symbol = CharacterToBioSymbol(bioValidator, seqdata[index]);
index++;
}
sequence.AlignedData.Add(symbol ?? BioSymbol.Gap);
}
}
internal FastASequence(FastAFile owner, bool loadAllIntoMemory, string header, long startPos, int length,
int firstNonGap, int count, IBioValidator validator)
{
Debug.Assert(header.Length > 0);
string[] bits = header.Split(new[] { "::" }, StringSplitOptions.None);
if (bits.Length == 3)
{
ScientificName = /*bits[0] +":" +*/ bits[1];
CommonName = bits[2];
}
else
{
ScientificName = header;
}
Validator = validator;
FirstDataColumn = firstNonGap;
if (string.IsNullOrEmpty(CommonName))
{
CommonName = "<Not Available>";
}
if (string.IsNullOrEmpty(ScientificName))
{
ScientificName = CommonName;
}
_dp = new FastAFileSequenceDataProvider(owner, startPos, length, count, validator);
if (loadAllIntoMemory)
{
_alignedList = new List <IBioSymbol>(_dp.LoadRange(0, length));
_dp.Dispose();
_dp = null;
}
else
{
_alignedList = new VirtualizingList <IBioSymbol>(_dp, Math.Min(1024, length), 60);
}
}
/// <summary>
/// This loads the sequences from the file
/// </summary>
/// <param name="bioValidator"></param>
/// <returns></returns>
private int LoadSequences(IBioValidator bioValidator)
{
_sequences.Clear();
using (var fs = File.OpenText(Filename))
{
string line = fs.ReadLine();
while (!string.IsNullOrEmpty(line))
{
// Header metadata?
if (Regex.IsMatch(line, HeaderRegex))
{
// Not loading metadata in this release.
//var headerLine = Regex.Match(line, HeaderRegex);
//if (headerLine.Groups["Statusin"].Value.Equals("in"))
//{
// string rowName = headerLine.Groups["Rowname"].Value;
//}
}
else if (!line.StartsWith("#-") && !line.StartsWith("#:") &&
Regex.IsMatch(line, SeqdataRowRegex))
{
LoadSequenceData(bioValidator, Regex.Match(line, SeqdataRowRegex));
}
line = fs.ReadLine();
}
}
// Calculate the first data column in each found sequence
Parallel.ForEach(_sequences.Cast <AE2Sequence>(), seq =>
{
seq.FirstDataColumn =
Enumerable.Range(0, seq.AlignedData.Count).FirstOrDefault(
i => seq.AlignedData[i].Type == BioSymbolType.Nucleotide);
});
return(_sequences.Count);
}
private static IBioSymbol CharacterToBioSymbol(IBioValidator bioValidator, char ch)
{
IBioSymbol symbol = null;
switch (ch)
{
case '~':
case '|':
symbol = BioSymbol.None;
break;
case '-':
symbol = BioSymbol.Gap;
break;
default:
if (bioValidator.IsValid(ch))
{
symbol = new BioSymbol(BioSymbolType.Nucleotide, ch);
}
break;
}
return(symbol);
}
/// <summary>
/// This loads the sequences from the file
/// </summary>
/// <param name="bioValidator"></param>
/// <returns></returns>
private int LoadSequences(IBioValidator bioValidator)
{
var headerBuffer = new byte[512];
string currHeader = string.Empty;
long startPos = -1;
int totalSequenceCount = 0, startingNonGap = -1;
bool loadIntoMemory = _loadAllIntoMemory || (new FileInfo(Filename).Length < SmallFileSize);
MmFile = MemoryMappedFile.CreateFromFile(Filename, FileMode.Open);
using (var fs = MmFile.CreateViewStream(0, 0, MemoryMappedFileAccess.Read))
{
for (; fs != null;)
{
int db = fs.ReadByte();
if (db <= 0)
{
break;
}
if ((char)db == '>') // Header for species?
{
// Just finished a sequence?
if (currHeader != string.Empty)
{
if (MaxSequenceLength < totalSequenceCount)
{
MaxSequenceLength = totalSequenceCount;
}
if (startingNonGap == -1)
{
startingNonGap = totalSequenceCount;
}
_sequences.Add(
new FastASequence(this, loadIntoMemory, currHeader, startPos,
(int)(fs.Position - startPos), startingNonGap, totalSequenceCount, bioValidator));
}
// Start new sequence
currHeader = string.Empty;
totalSequenceCount = 0;
startingNonGap = -1;
for (int i = 0; currHeader == string.Empty;)
{
db = fs.ReadByte();
if (db == -1 || db == 0x0a || db == 0x0d)
{
currHeader = Encoding.ASCII.GetString(headerBuffer, 0, i);
}
else
{
headerBuffer[i++] = (byte)db;
}
}
// This is the start of the nucleotide chain
startPos = fs.Position;
}
else if (db != 0x0a && db != 0x0d)
{
if (startingNonGap == -1 && bioValidator.IsValid((char)db))
{
startingNonGap = totalSequenceCount;
}
totalSequenceCount++;
}
}
// Handle the final sequence in the file.
Debug.Assert(currHeader != string.Empty);
Debug.Assert(totalSequenceCount > 0);
Debug.Assert(startPos > 0);
if (MaxSequenceLength < totalSequenceCount)
{
MaxSequenceLength = totalSequenceCount;
}
if (startingNonGap == -1)
{
startingNonGap = totalSequenceCount;
}
_sequences.Add(
new FastASequence(this, loadIntoMemory, currHeader, startPos,
(int)(fs.Position - startPos) - 1, startingNonGap, totalSequenceCount, bioValidator));
}
// Force all sequences to have the same "virtual" length
_sequences.ForEach(ns => ((FastASequence)ns).ForceLength(MaxSequenceLength));
if (loadIntoMemory)
{
MmFile.Dispose();
MmFile = null;
}
return(_sequences.Count);
}
public FastAFileSequenceDataProvider(FastAFile owner, long startPos, int length, int count, IBioValidator bv)
{
_fs = owner.MmFile.CreateViewStream(startPos, length, MemoryMappedFileAccess.Read);
_count = count;
_validator = bv;
}
public AE2Sequence(IBioValidator validator)
{
_alignedList = new List <IBioSymbol>();
Validator = validator;
}
